A general loss function is:
\begin{split}\text{obj} = \sum_{i=1}^n l(y_i, \hat{y}_i^{(t)}) + \sum_{i=1}^t\Omega(f_i) \\ \end{split}
which is prediction cost + regularization cost
A decision tree is defined as:
$f_t(x) = w_{q(x)}, w \in R^T, q:R^d\rightarrow \{1,2,\cdots,T\} $
Here w is the vector of scores on leaves, q is a function assigning each data point to the corresponding leaf, and T is the number of leaves. In XGBoost, we define the complexity as
$\Omega(f) = \gamma T + \frac{1}{2}\lambda \sum_{j=1}^T w_j^2$
so it seems to me that $w$'s are the final prediction scores for each leaf made by the decision tree. Under this understanding i get that xgboost is penalizing most confident predictions, even if correct, as part of the regularization term in the cost function.
I am not sure it even qualifies as a question as i am looking for someone to tell me if i am reading it right since i have never seen the confidence of a model being penalized under regularization
Also, are not the two parts of the cost function contradictory in some sense? With one part trying to be more confident and the other part (regularization part) in trying to be less confident